3dttest

Gosset (Student) t-test sets of 3D datasets

Usage 1: 3dttest [options] -set1 datasets ... -set2 datasets ...

for comparing the means of 2 sets of datasets (voxel by voxel).

Usage 2: 3dttest [options] -base1 bval -set2 datasets ...

for comparing the mean of 1 set of datasets against a constant.

OUTPUTS:

A single dataset is created that is the voxel-by-voxel difference

of the mean of set2 minus the mean of set1 (or minus 'bval').

The output dataset will be of the intensity+Ttest ('fitt') type.

The t-statistic at each voxel can be used as an interactive

thresholding tool in AFNI.

t-TESTING OPTIONS:

-set1 datasets ... = Specifies the collection of datasets to put into

the first set. The mean of set1 will be tested

with a 2-sample t-test against the mean of set2.

N.B.: -set1 and -base1 are mutually exclusive!

-base1 bval        = 'bval' is a numerical value that the mean of set2

will be tested against with a 1-sample t-test.

-set2 datasets ... = Specifies the collection of datasets to put into

the second set.  There must be at least 2 datasets

in each of set1 (if used) and set2.

-paired            = Specifies the use of a paired-sample t-test to

compare set1 and set2.  If this option is used,

set1 and set2 must have the same cardinality.

N.B.: A paired test is intended for use when the set1 and set2

dataset function values may be pairwise correlated.

If they are in fact uncorrelated, this test has less

statistical 'power' than the unpaired (default) t-test.

This loss of power is the price that is paid for

insurance against pairwise correlations.

-unpooled          = Specifies that the variance estimates for set1 and

set2 be computed separately (not pooled together).

This only makes sense if -paired is NOT given.

N.B.: If this option is used, the number of degrees

of freedom per voxel is a variable, rather

than a constant.  NOT RECOMMENDED.

-workmem mega      = 'mega' specifies the number of megabytes of RAM

to use for statistical workspace.  It defaults

to 12.  The program will run faster if this is

larger (see the NOTES section below).

The -base1 or -set1 command line switches must follow all other options

(including those described below) except for the -set2 switch.

INPUT EDITING OPTIONS: The same as are available in 3dmerge.

OUTPUT OPTIONS: these options control the output files.

-session  dirname  = Write output into given directory (default=./)

-prefix   pname    = Use 'pname' for the output directory prefix

(default=tdif)

-datum    type     = Use 'type' to store the output difference

in the means; 'type' may be short or float.

How the default is determined is described

in the notes below.

NOTES:

** To economize on memory, 3dttest makes multiple passes through

the input datasets.  On each pass, the entire editing process

will be carried out again.  For efficiency's sake, it is

better to carry out the editing using 3dmerge to produce

temporary datasets, and then run 3dttest on them.  This applies

with particular force if a 'blurring' option is used.

Note also that editing a dataset requires that it be read into

memory in its entirety (so that the disk file is not altered).

This will increase the memory needs of the program far beyond

the level set by the -workmem option.

** The input datasets are specified by their .HEAD files,

but their .BRIK files must exist also! This program cannot

'warp-on-demand' from other datasets.

** This program cannot deal with time-dependent or complex-valued datasets!

By default, the output dataset function values will be shorts if the

first input dataset is byte- or short-valued; otherwise they will be

floats.  This behavior may be overridden using the -datum option.

However, the t-statistic at each voxel will be always be

stored as a short integer that is 1000 times the actual t-value.

INPUT DATASET NAMES

-------------------

This program accepts datasets that are modified on input according to the

following schemes:

'r1+orig[3..5]'                                    {sub-brick selector}

'r1+orig<100.200>'                                 {sub-range selector}

'r1+orig[3..5]<100..200>'                          {both selectors}

'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )'  {calculation}

For the gruesome details, see the output of 'afni -help'.